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BCB Symposium - March 30, 2018

The Bioinformatics and Computational Biology Graduate Student Organization (BCBGSO) plans to hold a symposium for faculty and graduate students on March 30, 2018 from 8:30 to 5 p.m. at the ISU Alumni Center. Registration is now open.

The symposium is aimed at strengthening the collaborative interaction within and beyond the BCB community and facilitating the professional development of BCB graduate students. The theme of the symposium this year will be, “The Past and Future of Bioinformatics and Computational biology.” The four speakers who include past and present BCB Faculty members and two BCB alums, excellently reflect this theme:

Speaker PresentationsReiman Ballroom

9:15 – 10:05Volker Brendel

Exploring the transcriptional landscape of plant genomes

Initiation of transcription is the primary control point for gene expression. Traditional methods for probing gene expression (EST, RNAseq) provide only limited information about the precise locations of Transcription Start Sites (TSS). For plants, only a small number of genome-wide TSS profiling studies have been published. My group has developed computational workflows (Bioconductor package TSRchitect) for comprehensive, reproducible, and scalable analysis of TSS data sets that derive from any of the current experimental protocols. One advantage of our workflow design is that it allows for fair comparison and integration of data sets from different studies. I will discuss results for Arabidopsis and maize with respect to the distribution and characteristics of Transcription Start Regions (TSR). The ultimate goal of this work is to understand promoter architecture, function, and evolution in the context of gene expression networks.

10:10 – 11 a.m.
Matthew D. Wilkerson

The Molecular Characterization of Cancer

Cancer is the second leading cause of death worldwide as well as a significant burden on public health. Traditional cancer diagnostic tools do not regularly identify which tumors will lead to negative clinical outcome or identify exactly which patients will respond to particular therapies versus receive no benefit or have negative effects. A major challenge in this diagnosis are tumors’ vast morphologic, clinical and molecular heterogeneity. In order to comprehensively characterize cancers and ultimately advance cancer diagnosis, I have applied unsupervised classification and integrated bioinformatics analysis to large cohorts of tumors measured by multimodal genomics technologies during my research career. In lung squamous cell carcinoma, I discovered and validated the Basal, Classical, Secretory, and Primitive gene expression subtypes. These subtypes, which resemble distinct normal cell types in the lung, were found to be driven by distinct genomic alterations coordinated into pathways and are clinically-relevant as they predict differential patient survival. While I co-led the largest integrated molecular study on pheochromocytoma, application of these bioinformatics techniques discovered two novel subtypes, including the Wnt-altered subtype. Integrated analysis identified a new cancer driver gene, CSDE1, and identified fusion oncogenes in this disease for the first time – assigning a molecular basis to a new 7% of patients. The MAML3 fusion gene identified in our study is a new predictor of metastatic disease, in a disease with few such markers. Lastly, I will describe my new somatic mutation detector tool that combines DNA and RNA sequencing and leads to boosted sensitivity in low purity tumors, a particularly hard subset of cancer to characterize.

1 – 1:50
John Van Hemert

From Satellites to Sequencing: How Omics Fits Into the New Industrial Digital Agriculture

In 1905, when Edward Jenkins hired onto the scientific staff at the Connecticut Experiment Station Donald F. Jones, he said, “Young man, what can you do to improve corn? Connecticut needs a lot of milk. To get the milk we need lots of corn for our cows, and we lack good land to grow it.” Jones soon published the double-cross hybrid technique in 1918, which was adopted by Henry A. Wallace to found Pioneer in 1926. Today we continue to improve crop yield, stress tolerance, and more—not just to feed cows in Connecticut, but to feed a growing world human population. During this talk, I will describe some of the Precision Agriculture activities at DuPont Pioneer, ranging from satellite-based remote sensing to advanced plant imaging indoors to molecular characterization of the transcriptome and metabolome. Specifically, I will describe how we constructed data cubes of metabolomics and hyperspectral images to predict nitrogen response and yield in the field. I will also share how meta-analyses of many omics datasets have introduced new variation into the breeding and selection process.

1:55 – 2:45Adina Howe

There and back again: my academic journey

The academic job market is daunting. Securing and being successful in academia is associated with many challenges that can be overwhelming. No single perspective can prepare you on how to succeed in academic, but I will tell you about my journey to becoming an assistant professor at ISU and within BCB in the last few years. I'll highlight many challenges and successes of this adventure.

Other Symposium Program highlights

Additional plans for the day-long symposium include a poster session from 11 to noon in the Mente/Boyd Reception Area. Three student presentations will take place from 3 to 4 p.m. including Carla Mann from Drena Dobbs lab, Sayane Shome from Bob Jernigan's lab and Mingze He from Carolyn Lawrence Dill's lab.

Carolyn Lawrence Dill, chair of the BCB program, will give a A State of the Union for BCB address to end the day-long symposium. A social gathering will follow for speakers, current students and faculty of BCB.

These planned activities are intended to highlight the bioinformatics research being conducted at Iowa State University, as well as encourage collaborative connections within the bioinformatics community.

Complete Program for the BCB Symposium

Time

Item

8:30 - 9:00

Breakfast

9:00 - 9:15

Welcome and Opening Remarks (Alvin Chon)

9:15 – 10:05

Speaker 1 – Volker Brendel (Alvin Chon to introduce)

10:10 – 11

Speaker 2 – Matt Wilkerson (Valeria Velasquez Zapata to introduce)

11 – 12

Poster Session - Mente/Boyd Reception Area

12 – 1

Lunch

1 – 1:50

Speaker 3 – John Van Hemert (Devin Molnau to introduce)

1:55 – 2:45

Speaker 4 – Adina Howe (Paul Villanueva to introduce)

2:45 – 3

Break

3 – 4

Student Speakers – Carla Mann, Sayane Shome, Mingze He

4 – 4:15

The State of BCB: Dr. Carolyn Lawrence Dill

4:15 – 4:30

Closing Remarks (Sagnik Banerjee)

Support for the symposium has been provided by the Office of Biotechnology, the College of Liberal Arts and Sciences, The College of Agriculture and Life Sciences, the College of Veterinary Medicine, and the College of Engineering, as well as the Bioinformatics and Computational Biology Graduate Program, the Graduate & Professional Students Senate and ISU's Student Activities Center.